[ Started: 2023-04-09 04:52:14 CEST ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-beta/lib/R/library" Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 beta (2023-04-08 r84203) Old packages: 'BiocCheck', 'quantreg', 'rhdf5' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocCheck_1.35.18.tar.gz' Content type 'application/x-gzip' length 4374323 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://cloud.r-project.org/src/contrib/quantreg_5.95.tar.gz' Content type 'application/x-gzip' length 1026027 bytes (1001 KB) ================================================== downloaded 1001 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5_2.43.4.tar.gz' Content type 'application/x-gzip' length 1249046 bytes (1.2 MB) ================================================== downloaded 1.2 MB * installing *source* package ‘BiocCheck’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocCheck) * installing *source* package ‘quantreg’ ... ** package ‘quantreg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using Fortran compiler: ‘GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gfortran -fpic -g -O2 -c akj.f -o akj.o gfortran -fpic -g -O2 -c boot.f -o boot.o gfortran -fpic -g -O2 -c bound.f -o bound.o gfortran -fpic -g -O2 -c boundc.f -o boundc.o gfortran -fpic -g -O2 -c brute.f -o brute.o gfortran -fpic -g -O2 -c chlfct.f -o chlfct.o gfortran -fpic -g -O2 -c cholesky.f -o cholesky.o cholesky.f:2946:72: 2946 | IF ( NODE ) 400, 900, 500 | 1 Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) cholesky.f:2980:72: 2980 | IF ( RNODE ) 1100, 1800, 1200 | 1 Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) cholesky.f:3297:72: 3297 | IF ( ENODE ) 400, 800, 500 | 1 Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) cholesky.f:3354:72: 3354 | IF ( NODE ) 1000, 2100, 1100 | 1 Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) cholesky.f:3428:72: 3428 | IF ( NODE ) 1700, 2000, 1800 | 1 Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) gfortran -fpic -g -O2 -c combos.f -o combos.o gfortran -fpic -g -O2 -c crqf.f -o crqf.o crqf.f:98:72: 98 | DO 5 J=1,N | 1 Warning: Fortran 2018 deleted feature: Shared DO termination label 5 at (1) crqf.f:99:72: 99 | 5 WA(I,J) = X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 5 at (1) crqf.f:140:72: 140 | 25 WA(L,J) = X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 25 at (1) crqf.f:149:72: 149 | 50 SOL(J+1,1) = WF(J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 50 at (1) crqf.f:165:72: 165 | 60 XH(K,J) = X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 60 at (1) crqf.f:180:72: 180 | 80 S = S - WF(J)*X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 80 at (1) crqf.f:181:72: 181 | 90 WE(I) = S | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 90 at (1) crqf.f:192:72: 192 | 210 S = DMIN1(WD(J),S) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 210 at (1) crqf.f:205:72: 205 | 240 SOL(J+1,LSOL) = WF(J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 240 at (1) crqf.f:226:72: 226 | 250 WD(I) = ZERO | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 250 at (1) crqf.f:228:72: 228 | 260 WD(H(J)) = ONE | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 260 at (1) crqf.f:236:72: 236 | 270 S = S + X(I,J)*XH(J,KM) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 270 at (1) crqf.f:258:72: 258 | DO 310 J = 1,N | 1 Warning: Fortran 2018 deleted feature: Shared DO termination label 310 at (1) crqf.f:259:72: 259 | 310 XH(K,J) = X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 310 at (1) crqf.f:273:72: 273 | 330 S = S + XH(K,J)*Y(H(J)) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 330 at (1) crqf.f:274:72: 274 | 340 WF(K) = S | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 340 at (1) crqf.f:278:72: 278 | 350 S = S - WF(J)*X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 350 at (1) crqf.f:279:72: 279 | 360 WE(I) = S | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 360 at (1) crqf.f:287:72: 287 | 370 SOL(J+1,LSOL) = WF(J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 370 at (1) crqf.f:330:72: 330 | 396 B2 = B2 + X(I,J) * SOL(J+1,LSOL - 1) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 396 at (1) crqf.f:369:72: 369 | 506 WF(J) = ZERO | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 506 at (1) crqf.f:376:72: 376 | 510 WA(L1,J) = X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 510 at (1) crqf.f:379:72: 379 | 514 WF(J) = WF(J) + X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 514 at (1) crqf.f:389:72: 389 | 520 WF(J) = WF(J) + (ONE - W) * X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 520 at (1) crqf.f:394:72: 394 | 534 WA(MAL,J) = WF(J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 534 at (1) crqf.f:413:72: 413 | 540 XH(K,J) = X(I,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 540 at (1) crqf.f:429:72: 429 | 610 WD(I) = SOL(N+2,I) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 610 at (1) crqf.f:441:72: 441 | 650 WF(J) = S/V | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 650 at (1) crqf.f:445:72: 445 | 660 S = S + WF(J) * SOL(J+1,I) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 660 at (1) crqf.f:446:72: 446 | 670 SOL(N+2,I) = S | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 670 at (1) crqf.f:487:72: 487 | 60 A = A + X(I,K)*XH(K,J) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 60 at (1) crqf.f:488:72: 488 | 70 WA(I,J) = A | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 70 at (1) crqf.f:497:72: 497 | 90 IFLAG(I) = 0 | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 90 at (1) crqf.f:499:72: 499 | 95 IFLAG(H(J)) = 1 | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 95 at (1) crqf.f:544:72: 544 | 130 IFLAG(J) = IFLAG(J+M) | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 130 at (1) gfortran -fpic -g -O2 -c crqfnb.f -o crqfnb.o gfortran -fpic -g -O2 -c dsel05.f -o dsel05.o gfortran -fpic -g -O2 -c etime.f -o etime.o gfortran -fpic -g -O2 -c extract.f -o extract.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c frand.c -o frand.o gfortran -fpic -g -O2 -c grexp.f -o grexp.o gfortran -fpic -g -O2 -c idmin.f -o idmin.o gfortran -fpic -g -O2 -c iswap.f -o iswap.o iswap.f:40:72: 40 | IF (INCX-1) 5,20,60 | 1 Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) gfortran -fpic -g -O2 -c kuantile.f -o kuantile.o gfortran -fpic -g -O2 -c kuantiles.f -o kuantiles.o gfortran -fpic -g -O2 -c linpack.f -o linpack.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mcmb.c -o mcmb.o gfortran -fpic -g -O2 -c penalty.f -o penalty.o gfortran -fpic -g -O2 -c pfnb.f -o pfnb.o gfortran -fpic -g -O2 -c powell.f -o powell.o gfortran -fpic -g -O2 -c profnb.f -o profnb.o gfortran -fpic -g -O2 -c pwxy.f -o pwxy.o gfortran -fpic -g -O2 -c qfnb.f -o qfnb.o gfortran -fpic -g -O2 -c qselect.f -o qselect.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c quantreg_init.c -o quantreg_init.o gfortran -fpic -g -O2 -c rls.f -o rls.o gfortran -fpic -g -O2 -c rq0.f -o rq0.o gfortran -fpic -g -O2 -c rq1.f -o rq1.o gfortran -fpic -g -O2 -c rqbr.f -o rqbr.o gfortran -fpic -g -O2 -c rqfn.f -o rqfn.o gfortran -fpic -g -O2 -c rqfnb.f -o rqfnb.o gfortran -fpic -g -O2 -c rqfnc.f -o rqfnc.o gfortran -fpic -g -O2 -c rqs.f -o rqs.o gfortran -fpic -g -O2 -c sakj.f -o sakj.o gfortran -fpic -g -O2 -c sparskit2.f -o sparskit2.o gfortran -fpic -g -O2 -c srqfn.f -o srqfn.o gfortran -fpic -g -O2 -c srqfnc.f -o srqfnc.o gfortran -fpic -g -O2 -c srtpai.f -o srtpai.o srtpai.f:19:72: 19 | 10 P(1, I) = I | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1) gcc -shared -L/usr/local/lib -o quantreg.so akj.o boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crqf.o crqfnb.o dsel05.o etime.o extract.o frand.o grexp.o idmin.o iswap.o kuantile.o kuantiles.o linpack.o mcmb.o penalty.o pfnb.o powell.o profnb.o pwxy.o qfnb.o qselect.o quantreg_init.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o rqs.o sakj.o sparskit2.o srqfn.o srqfnc.o srtpai.o -llapack -L/opt/R-beta/lib/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.3-3.17/00LOCK-quantreg/00new/quantreg/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (quantreg) * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5.c -o H5.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5A.c -o H5A.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5D.c -o H5D.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5E.c -o H5E.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5F.c -o H5F.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5G.c -o H5G.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5I.c -o H5I.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5L.c -o H5L.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5O.c -o H5O.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5P.c -o H5P.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5R.c -o H5R.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S.c -o H5S.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S_extras.c -o H5S_extras.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5T.c -o H5T.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5Z.c -o H5Z.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5constants.c -o H5constants.o g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleList.cpp -o HandleList.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleListWrap.c -o HandleListWrap.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c bit64conversion.c -o bit64conversion.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c external_filters.c -o external_filters.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5dump.c -o h5dump.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5ls.c -o h5ls.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5testLock.c -o h5testLock.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c printdatatype.c -o printdatatype.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c wrap.c -o wrap.o g++ -std=gnu++17 -shared -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/omnipath/local/R/4.3-3.17/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm installing to /home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5/00new/rhdf5/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5) The downloaded source packages are in ‘/tmp/RtmpNiCdgo/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 beta (2023-04-08 r84203) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr [ Finished: 2023-04-09 04:52:46 CEST ]